Evaluating functional network inference using simulations of complex biological systems.

MOTIVATION: Although many network inference algorithms have been presented in the bioinformatics literature, no suitable approach has been formulated for evaluating their effectiveness at recovering models of complex biological systems from limited data. To overcome this limitation, we propose an approach to evaluate network inference algorithms according to their ability to recover a complex functional network from biologically reasonable simulated data. RESULTS: We designed a simulator to generate data representing a complex biological system at multiple levels of organization: behaviour, neural anatomy, brain electrophysiology, and gene expression of songbirds. About 90% of the simulated variables are unregulated by other variables in the system and are included simply as distracters. We sampled the simulated data at intervals as one would sample from a biological system in practice, and then used the sampled data to evaluate the effectiveness of an algorithm we developed for functional network inference. We found that our algorithm is highly effective at recovering the functional network structure of the simulated system-including the irrelevance of unregulated variables-from sampled data alone. To assess the reproducibility of these results, we tested our inference algorithm on 50 separately simulated sets of data and it consistently recovered almost perfectly the complex functional network structure underlying the simulated data. To our knowledge, this is the first approach for evaluating the effectiveness of functional network inference algorithms at recovering models from limited data. Our simulation approach also enables researchers a priori to design experiments and data-collection protocols that are amenable to functional network inference.

Bulk synchronous parallelization of industrial electromagentic software

The parallelization of existing/industrial electromagnetic software using the bulk synchronous parallel (BSP) computation model is presented. The software employs the finite element method with a preconditioned conjugate gradient-type solution for the resulting linear systems of equations. A geometric mesh-partitioning approach is applied within the BSP framework for the assembly and solution phases of the finite element computation. This is combined with a nongeometric, data-driven parallel quadrature procedure for the evaluation of right-hand-side terms in applications involving coil fields. A similar parallel decomposition is applied to the parallel calculation of electron beam trajectories required for the design of tube devices. The BSP parallelization approach adopted is fully portable, conceptually simple, and cost-effective, and it can be applied to a wide range of finite element applications not necessarily related to electromagnetics.

Design process knowledge reuse challenges and issues

Product knowledge support needs are compared in two companies with different production volumes and product complexity. Knowledge support requirements identified include: function, performance data, requirements data, common parts, regulatory guidelines and layout data. A process based data driven knowledge reuse method is evaluated in light of the identified product knowledge needs. The evaluation takes place through developing a pilot case with each company. It is found that the method provides more benefit to the high complexity design domain, in which a significant amount of work takes place at the conceptual design stages, relying on a conceptual product representation. There is not such a clear value proposition in a design environment whose main challenge is layout design and the application of standard parts and features. The method supports the requirement for conceptual product representation but does not fully support a standard parts library.

The Paediatric Rheumatology International Trials Organisation provisional criteria for the evaluation of response to therapy in juvenile dermatomyositis.

Objective To develop a provisional definition for the evaluation of response to therapy in juvenile dermatomyositis (DM) based on the Paediatric Rheumatology International Trials Organisation juvenile DM core set of variables. Methods Thirty-seven experienced pediatric rheumatologists from 27 countries achieved consensus on 128 difficult patient profiles as clinically improved or not improved using a stepwise approach (patient's rating, statistical analysis, definition selection). Using the physicians' consensus ratings as the “gold standard measure,” chi-square, sensitivity, specificity, false-positive and-negative rates, area under the receiver operating characteristic curve, and kappa agreement for candidate definitions of improvement were calculated. Definitions with kappa values >0.8 were multiplied by the face validity score to select the top definitions. Results The top definition of improvement was at least 20% improvement from baseline in 3 of 6 core set variables with no more than 1 of the remaining worsening by more than 30%, which cannot be muscle strength. The second-highest scoring definition was at least 20% improvement from baseline in 3 of 6 core set variables with no more than 2 of the remaining worsening by more than 25%, which cannot be muscle strength (definition P1 selected by the International Myositis Assessment and Clinical Studies group). The third is similar to the second with the maximum amount of worsening set to 30%. This indicates convergent validity of the process. Conclusion We propose a provisional data-driven definition of improvement that reflects well the consensus rating of experienced clinicians, which incorporates clinically meaningful change in core set variables in a composite end point for the evaluation of global response to therapy in juvenile DM.

Computational Verification of Two Universal Relations for Simple Ionic Liquids. Kinetic Properties of a Model 2:1 Molten Salt

Two semianalytical relations [Nature, 1996, 381, 137 and Phys. Rev. Lett. 2001, 87, 245901] predicting dynamical coefficients of simple liquids on the basis of structural properties have been tested by extensive molecular dynamics simulations for an idealized 2:1 model molten salt. In agreement with previous simulation studies, our results support the validity of the relation expressing the self-diffusion coefficient as a Function of the radial distribution functions for all thermodynamic conditions such that the system is in the ionic (ie., fully dissociated) liquid state. Deviations are apparent for high-density samples in the amorphous state and in the low-density, low-temperature range, when ions condense into AB(2) molecules. A similar relation predicting the ionic conductivity is only partially validated by our data. The simulation results, covering 210 distinct thermodynamic states, represent an extended database to tune and validate semianalytical theories of dynamical properties and provide a baseline for the interpretation of properties of more complex systems such as the room-temperature ionic liquids.

A study of the relational aspects of the culture of academic medicine

PURPOSE: The impact of medical school culture on medical students has been well studied, but little documentation exists regarding how medical faculty experience the culture in which they work. In an ongoing project, the National Initiative on Gender, Culture and Leadership in Medicine, the authors are investigating how the existing culture of academic medical institutions supports all faculty members' ability to function at their highest potential. METHOD: The authors conducted a qualitative study of faculty in five disparate U.S. medical schools. Faculty in different career stages and diverse specialties were interviewed regarding their perceptions and experiences in academic medicine. Analysis was inductive and data driven. RESULTS: Relational aspects of the culture emerged as a central theme for both genders across all career categories. Positive relationships were most evident with patients and learners. Negative relational attributes among faculty and leadership included disconnection, competitive individualism, undervaluing of humanistic qualities, deprecation, disrespect, and the erosion of trust. CONCLUSIONS: The data suggest that serious problems exist in the relational culture and that such problems may affect medical faculty vitality, professionalism, and general productivity and are linked to retention. Efforts to create and support trusting relationships in medical schools might enhance all faculty members' efforts to optimally contribute to the clinical, education, and research missions of academic medicine. Future work will document the outcomes of a five-school collaboration to facilitate change in the culture to support the productivity of all medical faculty. © 2009 Association of American Medical Colleges.

WIQ:Work-intensive query scheduling for in-memory database systems

We propose a novel admission control policy for database queries. Our methodology uses system measurements of CPU utilization and query backlogs to determine interference between queries in execution on the same database server. Query interference may arise due to the concurrent access of hardware and software resources and can affect performance in positive and negative ways. Specifically our admission control considers the mix of jobs in service and prioritizes the query classes consuming CPU resources more efficiently. The policy ignores I/O subsystems and is therefore highly appropriate for in-memory databases. We validate our approach in trace-driven simulation and show performance increases of query slowdowns and throughputs compared to first-come first-served and shortest expected processing time first scheduling. Simulation experiments are parameterized from system traces of a SAP HANA in-memory database installation with TPC-H type workloads. © 2012 IEEE.

IO Performance Prediction in Consolidated Virtualized Environments

We propose a trace-driven approach to predict the performance degradation of disk request response times due to storage device contention in consolidated virtualized environments. Our performance model evaluates a queueing network with fair share scheduling using trace-driven simulation. The model parameters can be deduced from measurements obtained inside Virtual Machines (VMs) from a system where a single VM accesses a remote storage server. The parameterized model can then be used to predict the effect of storage contention when multiple VMs are consolidated on the same virtualized server. The model parameter estimation relies on a search technique that tries to estimate the splitting and merging of blocks at the the Virtual Machine Monitor (VMM) level in the case of multiple competing VMs. Simulation experiments based on traces of the Postmark and FFSB disk benchmarks show that our model is able to accurately predict the impact of workload consolidation on VM disk IO response times.

Personalized medicine: Has it started yet? A reconstruction of the early history

Within the last few years the field personalized medicine entered the stage. Accompanied with great hopes and expectations it is believed that this field may have the potential to revolutionize medical and clinical care by utilizing genomics information about the individual patients themselves. In this paper, we reconstruct the early footprints of personalized medicine as reflected by information retrieved from PubMed and Google Scholar. That means we are providing a data-driven perspective of this field to estimate its current status and potential problems.

Generalized Laplacian Eigenmaps for Modeling and Tracking Human Motions

This paper presents generalized Laplacian eigenmaps, a novel dimensionality reduction approach designed to address stylistic variations in time series. It generates compact and coherent continuous spaces whose geometry is data-driven. This paper also introduces graph-based particle filter, a novel methodology conceived for efficient tracking in low dimensional space derived from a spectral dimensionality reduction method. Its strengths are a propagation scheme, which facilitates the prediction in time and style, and a noise model coherent with the manifold, which prevents divergence, and increases robustness. Experiments show that a combination of both techniques achieves state-of-the-art performance for human pose tracking in underconstrained scenarios.

Energy monitoring and quality control of a single screw extruder

Polymer extrusion, in which a polymer is melted and conveyed to a mould or die, forms the basis of most polymer processing techniques. Extruders frequently run at non-optimised conditions and can account for 15–20% of overall process energy losses. In times of increasing energy efficiency such losses are a major concern for the industry. Product quality, which depends on the homogeneity and stability of the melt flow which in turn depends on melt temperature and screw speed, is also an issue of concern of processors. Gear pumps can be used to improve the stability of the production line, but the cost is usually high. Likewise it is possible to introduce energy meters but they also add to the capital cost of the machine. Advanced control incorporating soft sensing capabilities offers opportunities to this industry to improve both quality and energy efficiency. Due to strong correlations between the critical variables, such as the melt temperature and melt pressure, traditional decentralized PID (Proportional–Integral–Derivative) control is incapable of handling such processes if stricter product specifications are imposed or the material is changed from one batch to another. In this paper, new real-time energy monitoring methods have been introduced without the need to install power meters or develop data-driven models. The effects of process settings on energy efficiency and melt quality are then studied based on developed monitoring methods. Process variables include barrel heating temperature, water cooling temperature, and screw speed. Finally, a fuzzy logic controller is developed for a single screw extruder to achieve high melt quality. The resultant performance of the developed controller has shown it to be a satisfactory alternative to the expensive gear pump. Energy efficiency of the extruder can further be achieved by optimising the temperature settings. Experimental results from open-loop control and fuzzy control on a Killion 25 mm single screw extruder are presented to confirm the efficacy of the proposed approach.

Handbook of International Special Education:Northern Ireland

The intent of the Handbook of International Special Education is to provide a concise overview of special education services in countries across the world using the Article on Education in the United Nations Convention on the Rights of Persons with Disabilities as the analytical frame. The Handbook will provide concise, data-driven contributions from across the globe using two primary frames: the relationship between special and general education in the country and the country’s system as aligned with the Article on Education in the UN Convention on the Rights of Person with Disabilities.

Face Recognition in the Scrambled Domain via Salience-Aware Ensembles of Many Kernels

With the rapid development of internet-of-things (IoT), face scrambling has been proposed for privacy protection during IoT-targeted image/video distribution. Consequently in these IoT applications, biometric verification needs to be carried out in the scrambled domain, presenting significant challenges in face recognition. Since face models become chaotic signals after scrambling/encryption, a typical solution is to utilize traditional data-driven face recognition algorithms. While chaotic pattern recognition is still a challenging task, in this paper we propose a new ensemble approach – Many-Kernel Random Discriminant Analysis (MK-RDA) to discover discriminative patterns from chaotic signals. We also incorporate a salience-aware strategy into the proposed ensemble method to handle chaotic facial patterns in the scrambled domain, where random selections of features are made on semantic components via salience modelling. In our experiments, the proposed MK-RDA was tested rigorously on three human face datasets: the ORL face dataset, the PIE face dataset and the PUBFIG wild face dataset. The experimental results successfully demonstrate that the proposed scheme can effectively handle chaotic signals and significantly improve the recognition accuracy, making our method a promising candidate for secure biometric verification in emerging IoT applications.

An integrated framework for combining gist vision with object segregation categorisation and recognition

There are roughly two processing systems: (1) very fast gist vision of entire scenes, completely bottom-up and data driven, and (2) Focus-of-Attention (FoA) with sequential screening of specific image regions and objects. The latter system has to be sequential because unnormalised input objects must be matched against normalised templates of canonical object views stored in memory, which involves dynamic routing of features in the visual pathways.

Soft-computing techniques applied to artificial tissue temperature estimation

Tese dout., Engenharia electrónica e computação - Processamento de sinal, Universidade do Algarve, 2008